4. The Submarine Conundrum - Raiders Of The Lost Ark
The Confusing Moment:
He might be something of a superhero, but there's no way Indiana Jones could have clung onto a submarine underwater for the entire time he manages to in Raiders Of The Lost Ark. He would have been thrown off or drowned were it not for the unsatisfying explanation of his impenetrable plot armour.
The Deleted Scene:
Actually, he didn't just hold his breath for a superhuman amount of time. In Lawrence's Kasdan's original script, the submarine is only submerged to the point that its periscope sticks out of the water, which Indy clings to and then lashes himself to with his whip.
As any U-Boat historian would tell you, most of the time the vessels didn't submerge most of the time anyway, as their very design meant they were suited more to being on the surface.